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EBIvariation / opentargets-pharmgkb

Pipeline to provide evidence strings for Open Targets from PharmGKB
Apache License 2.0
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Map phenotypes to EFO terms #4

Closed apriltuesday closed 1 year ago

apriltuesday commented 1 year ago

This should not use manual curation (yet), only primary data provided by PharmGKB or exact/high confidence mappings from OLS or OxO.

apriltuesday commented 1 year ago

External vocabulary / cross references in phenotypes.tsv (primary data from PGKB) doesn't seem to contain any of our supported ontologies; crossrefs I see are SnoMed, UMLS, MeSH, NDFRT (example). We might be able to use these to get better mapping coverage but I think it's out of scope for the first attempt.